CPPTRAJ: Trajectory Analysis. V16.00b OpenMP ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 05/25/16 15:40:45 | Available memory: 16.021 GB INPUT: Reading input from 'pt-clust.in' [parm ../../tip3p/ff12sb/run1/build/full.topo.hmr [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/build/full.topo.hmr' as Amber Topology [trajin ../../tip3p/ff12sb/run1/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run1/traj.1.02,../../tip3p/ff12sb/run1/traj.1.03,../../tip3p/ff12sb/run1/traj.1.04,../../tip3p/ff12sb/run1/traj.1.05,../../tip3p/ff12sb/run1/traj.1.06,../../tip3p/ff12sb/run1/traj.1.07,../../tip3p/ff12sb/run1/traj.1.08,../../tip3p/ff12sb/run1/traj.1.09,../../tip3p/ff12sb/run1/traj.1.10,../../tip3p/ff12sb/run1/traj.1.11,../../tip3p/ff12sb/run1/traj.1.12,../../tip3p/ff12sb/run1/traj.1.13,../../tip3p/ff12sb/run1/traj.1.14,../../tip3p/ff12sb/run1/traj.1.15,../../tip3p/ff12sb/run1/traj.1.16,../../tip3p/ff12sb/run1/traj.1.17,../../tip3p/ff12sb/run1/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run1/traj.1.01' as Amber NetCDF [trajin ../../tip3p/ff12sb/run2/traj.1.01 remdtraj remdtrajtemp 298.41 trajnames ../../tip3p/ff12sb/run2/traj.1.02,../../tip3p/ff12sb/run2/traj.1.03,../../tip3p/ff12sb/run2/traj.1.04,../../tip3p/ff12sb/run2/traj.1.05,../../tip3p/ff12sb/run2/traj.1.06,../../tip3p/ff12sb/run2/traj.1.07,../../tip3p/ff12sb/run2/traj.1.08,../../tip3p/ff12sb/run2/traj.1.09,../../tip3p/ff12sb/run2/traj.1.10,../../tip3p/ff12sb/run2/traj.1.11,../../tip3p/ff12sb/run2/traj.1.12,../../tip3p/ff12sb/run2/traj.1.13,../../tip3p/ff12sb/run2/traj.1.14,../../tip3p/ff12sb/run2/traj.1.15,../../tip3p/ff12sb/run2/traj.1.16,../../tip3p/ff12sb/run2/traj.1.17,../../tip3p/ff12sb/run2/traj.1.18 parm [tip3p-ff12sb]] Reading '../../tip3p/ff12sb/run2/traj.1.01' as Amber NetCDF [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [rmsd :1-2&!@H= first mass out test.dat] RMSD: (:1-2&!@H*), reference is first frame (:1-2&!@H*), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] CLUSTER: Using coords dataset _DEFAULTCRD_, clustering using RMSD (mask [:1,2&!@H=]) best-fit K-MEANS: Looking for 7 clusters. Sequentially modify each point. Cluster to cluster distance will be based on cluster centroids. Initial clustering will be randomly sieved (with value 200). Previously calcd pair distances CpptrajPairDist will be used if found. Summary of cluster results will be written to clust-summary.dat Summary comparing parts of trajectory data for clusters will be written to split.dat Frames will be split at: 50000 100000 Cluster trajectories will be written to ctraj, format Amber NetCDF Cluster representatives will be written to separate trajectories, prefix (rep), format PDB Warning: One or more analyses requested creation of default COORDS DataSet. CREATECRD: Saving coordinates from Top full.topo.hmr to "_DEFAULTCRD_" ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: [tip3p-ff12sb] full.topo.hmr, 3296 atoms, 1088 res, box: Orthogonal, 1087 mol, 1075 solvent INPUT TRAJECTORIES (2 total): 0: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K 1: REMD trajectories (18 total), lowest replica 'traj.1.01' (reading 50000 of 50000) Looking for frames at 298.41 K Coordinate processing will occur on 100000 frames. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM 'full.topo.hmr' (4 actions): 0: [autoimage origin] Anchor molecule is 1 1086 molecules are mobile. 1: [strip :WAT,Na+,Cl-] Stripping 3236 atoms. Stripped topology: 60 atoms, 2 res, box: Orthogonal, 1 mol 2: [rmsd :1-2&!@H= first mass out test.dat] Target mask: [:1-2&!@H*](37) Reference mask: [:1-2&!@H*](37) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [createcrd _DEFAULTCRD_] Warning: COORDS data sets do not store temperatures. Warning: COORDS data sets do not store times. Estimated memory usage (100000 frames): 74.400 MB ----- traj.1.01 (1-50000, 1) ----- 0% 10% 20% 30% 40% ----- traj.1.01 (1-50000, 1) ----- 50% 60% 70% 80% 90% 100% Complete. Read 100000 frames and processed 100000 frames. TIME: Avg. throughput= 25.7472 frames / second. ACTION OUTPUT: ANALYSIS: Performing 1 analyses: 0: [cluster :1,2&!@H= summary clust-summary.dat repout rep repfmt pdb clusterout ctraj clusterfmt netcdf kmeans clusters 7 sieve 200 random savepairdist pairdist CpptrajPairDist summaryhalf split.dat splitframe 50000,100000] Starting clustering. Mask [:1,2&!@H*] corresponds to 37 atoms. Calculating pair-wise distances. Random_Number: seed is <= 0, using wallclock time as seed (183410000) Estimated pair-wise matrix memory usage: > 499.064 kB Pair-wise matrix set up with sieve, 100000 frames, 500 sieved frames. 0% 11% 21% 30% 41% 51% 61% 70% 81% 91% Complete. Saving pair-wise distances to CpptrajPairDist Memory used by pair-wise matrix and other cluster data: 999.160 kB Round 0: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 0: 493 points changed cluster assignment. Round 1: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 1: 21 points changed cluster assignment. Round 2: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 2: 22 points changed cluster assignment. Round 3: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 3: 38 points changed cluster assignment. Round 4: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 4: 71 points changed cluster assignment. Round 5: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 5: 50 points changed cluster assignment. Round 6: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 6: 10 points changed cluster assignment. Round 7: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 7: 6 points changed cluster assignment. Round 8: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 8: 1 points changed cluster assignment. Round 9: 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. K-means round 9: No change. Skipping the rest of the iterations. Restoring sieved frames. Parallelizing calculation with 8 threads 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% Complete. #Clustering: 7 clusters 100000 frames #Cluster 0 has average-distance-to-centroid 0.825197 #Cluster 1 has average-distance-to-centroid 0.731911 #Cluster 2 has average-distance-to-centroid 1.371621 #Cluster 3 has average-distance-to-centroid 1.154145 #Cluster 4 has average-distance-to-centroid 1.134848 #Cluster 5 has average-distance-to-centroid 1.383401 #Cluster 6 has average-distance-to-centroid 1.479361 #DBI: 1.240045 #pSF: 37543.540832 #Algorithm: Kmeans nclusters 7 maxit 100 #Representative frames: 64074 19198 80437 75418 4434 77349 5412 #Sieve value: 200 (random) #Sieved frames: 93 150 298 671 696 1128 1507 1643 1939 2039 2316 2576 2737 3046 3105 3166 3664 4070 4434 4650 4768 4872 5412 5441 5588 5666 5953 5962 5978 6194 6536 6566 6657 6877 6906 6973 7149 7398 7403 7570 7642 7877 8351 9015 9087 9574 9656 9712 9750 10013 10349 10366 10535 10687 10958 11017 12290 12295 12518 12672 12694 12940 13404 13440 13752 13842 13863 13972 14009 14276 14370 14498 14616 14625 14629 15030 15049 15222 15433 15444 15682 15804 16558 16563 16885 16989 17149 17333 17415 17570 17678 17794 18068 18175 18617 19198 19276 19364 19511 19514 19700 19795 20049 20562 20735 21442 21551 21907 22028 22112 22221 22320 22339 22632 23039 23044 23064 23468 23536 23860 24373 24717 24796 25146 25180 25356 25375 25620 25734 25867 26206 26489 26602 26810 26854 27259 27299 27647 27809 28573 28607 29096 29137 29533 29536 29621 29811 29815 29893 29928 29999 30115 30397 30503 30819 30834 31496 31537 31959 32071 32199 32410 32553 32579 32925 32934 33057 33347 34040 34043 34367 34468 34541 35415 35502 35786 35853 36015 36181 36790 36856 37570 37687 37881 37951 38124 38375 38697 38713 38804 39245 39609 39692 39704 39844 39961 40048 40364 40784 41005 41027 41098 41279 41578 41757 41843 41886 41995 42483 42900 42930 43066 43146 43232 43241 43908 44079 44464 45073 45189 45329 45637 45715 45764 45816 46117 46173 46707 47129 47203 47331 47404 47443 47683 48517 48526 48557 48567 48611 48711 49854 49876 50093 50282 50531 51283 51879 52102 52310 52334 52559 52605 52630 52781 52783 52802 53190 53314 53845 54011 54226 54390 54400 54409 54587 54642 54675 54837 54838 54839 54987 55329 55845 56224 56297 56442 57110 57156 57160 57243 57711 57902 58384 58649 58737 58867 58928 58995 59028 59176 59219 59474 59667 60184 60286 60704 60833 61343 61502 61693 61739 61787 62020 62059 62184 62753 62756 62857 62975 63019 63461 63566 63708 63988 64061 64074 64425 64864 65315 65522 65639 65646 65726 65955 66367 66446 66549 67039 67240 67255 67636 68499 68552 68595 68810 68958 69071 69134 69607 69721 69857 69939 69947 70132 70583 70630 70782 70823 71170 71196 71615 71966 72072 72168 72346 72365 72550 72822 73169 73451 73453 73616 73740 74280 74463 74539 74643 74733 74884 75180 75307 75418 75462 75725 75877 76043 76695 77035 77086 77309 77349 77428 77501 77605 77725 77899 77931 78200 78209 78220 78320 78990 79337 79403 80118 80415 80437 80549 80555 80567 80618 80636 80705 81062 81069 81243 81334 81368 81378 81382 81512 81795 82229 82474 82570 83272 83372 83407 83646 83824 84222 84393 84998 85483 85553 85654 85814 85960 86202 86203 86204 86280 86458 86652 86922 87159 87208 87469 87906 87944 88210 88354 88483 88711 89014 89015 89160 89774 89888 89965 90518 90989 91099 91435 91834 92025 92027 92207 92208 92259 92559 92861 92961 93093 93103 93691 93695 93755 94150 94257 94330 94530 94737 95123 95268 95385 95462 95470 95481 95759 95829 95840 96073 96352 96446 96802 96940 97489 97519 97540 97642 97946 98109 98115 98419 98613 98944 99106 99141 99438 Warning: split frame 100000 is out of bounds; ignoring. Writing 'ctraj.c0' as Amber NetCDF Writing 'ctraj.c1' as Amber NetCDF Writing 'ctraj.c2' as Amber NetCDF Writing 'ctraj.c3' as Amber NetCDF Writing 'ctraj.c4' as Amber NetCDF Writing 'ctraj.c5' as Amber NetCDF Writing 'ctraj.c6' as Amber NetCDF Writing 'rep.c0.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c1.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c2.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c3.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c4.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c5.pdb' as PDB Warning: No PDB space group specified. Writing 'rep.c6.pdb' as PDB Warning: No PDB space group specified. Cluster timing data: TIME: Cluster Init. : 0.3221 s ( 0.46%) TIME: Pairwise Calc.: 0.1176 s ( 0.17%) TIME: Clustering : 0.1369 s ( 0.19%) TIME: Cluster Post. : 69.9715 s ( 99.18%) TIME: Total: 70.5482 s TIME: Analyses took 70.5482 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 100000 _DEFAULTCRD_ "_DEFAULTCRD_" (coordinates), size is 100000 (74.400 MB) Box Coords, 60 atoms Cnum_00003 "Cnum_00003" (integer), size is 100000 DATAFILES (1 total): test.dat (Standard Data File): RMSD_00001 RUN TIMING: TIME: Init : 0.0000 s ( 0.00%) TIME: Trajectory Process : 3883.9223 s ( 98.21%) TIME: Action Post : 0.0000 s ( 0.00%) TIME: Analysis : 70.5482 s ( 1.78%) TIME: Data File Write : 0.1630 s ( 0.00%) TIME: Other : 0.0002 s ( 0.00%) TIME: Run Total 3954.6338 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 3957.3926 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.